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(-) Description

Title :  CRYSTAL STRUCTURE OF INPP5B IN COMPLEX WITH PHOSPHATIDYLINOSITOL 4-PHOSPHATE
 
Authors :  L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, S. Kol, T. Kotenyova, M. Moche, T. Nyman, C. Persson, H. Sc P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg J. Weigelt, M. Wisniewska, P. Nordlund, Structural Genomics Conso (Sgc)
Date :  30 Apr 10  (Deposition) - 30 Jun 10  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Inpp5Ba, Phosphoinositide 5-Phosphatase, Inositol Signalling, Phosphatase, Magnesium, Structural Genomics, Sgc, Sgc Stockholm, Structural Genomics Consortium, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Tresaugues, C. Silvander, S. Flodin, M. Welin, T. Nyman, S. Graslund, M. Hammarstrom, H. Berglund, P. Nordlund
Structural Basis For Phosphoinositide Substrate Recognition Catalysis, And Membrane Interactions In Human Inositol Polyphosphate 5-Phosphatases
Structure V. 22 744 2014
PubMed-ID: 24704254  |  Reference-DOI: 10.1016/J.STR.2014.01.013

(-) Compounds

Molecule 1 - TYPE II INOSITOL-1,4,5-TRISPHOSPHATE 5-PHOSPHATASE
    ChainsA
    EC Number3.1.3.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CH2
    Expression System StrainBL21 (DE3) R3 PRARE
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 339-643
    GeneINPP5B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHOINOSITIDE 5-PHOSPHATASE, 5PTASE, 75 KDA INOSITOL POLYPHOSPHATE-5-PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4PIF1Ligand/Ion(2R)-3-{[(S)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-TETRAHYDROXY-4-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYLDIOCTANOATE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PIF1Ligand/Ion(2R)-3-{[(S)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-TETRAHYDROXY-4-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYLDIOCTANOATE
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PIF3Ligand/Ion(2R)-3-{[(S)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-TETRAHYDROXY-4-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYLDIOCTANOATE
5SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:41 , HOH A:109 , ILE A:262 , GLN A:263 , HIS A:357 , TYR A:360 , HIS A:390 , ASN A:532BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREHOH A:77 , HOH A:78 , HOH A:79 , ASN A:275 , GLU A:303 , PIF A:572BINDING SITE FOR RESIDUE MG A 571
3AC3SOFTWAREHOH A:70 , HOH A:73 , HOH A:74 , HOH A:75 , HOH A:76 , HOH A:78 , HOH A:87 , HOH A:174 , GLU A:303 , LEU A:306 , ASN A:379 , LYS A:380 , HIS A:400 , HIS A:404 , TYR A:502 , LYS A:503 , LYS A:516 , ARG A:518 , MG A:571BINDING SITE FOR RESIDUE PIF A 572
4AC4SOFTWAREHOH A:93 , HOH A:94 , HOH A:191 , SER A:307 , LYS A:308 , ARG A:376BINDING SITE FOR RESIDUE SO4 A 573
5AC5SOFTWAREHOH A:192 , GLY A:372 , ILE A:373 , MET A:374 , ARG A:410BINDING SITE FOR RESIDUE GOL A 574
6AC6SOFTWAREHIS A:541 , ALA A:543BINDING SITE FOR RESIDUE CL A 575

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MTC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:502 -Lys A:503

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MTC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MTC)

(-) Exons   (0, 0)

(no "Exon" information available for 3MTC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:310
 aligned with I5P2_HUMAN | P32019 from UniProtKB/Swiss-Prot  Length:993

    Alignment length:310
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647
           I5P2_HUMAN   338 DYTYIQNFRFFAGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVNDEL 647
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee.........hhhhhh.......eeeeeee....hhhhhh....hhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeee.hhhh.eeeeeeeeee.hhhhh....eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhh..................eeeeeee........hhhhhhhhhhh.hhhhhhh.hhhhhhhhh.......................................eeeeeee..eeeeeeee...........eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mtc A 258 MYTYIQNFRFFAGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVAHHH 567
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3MTC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MTC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MTC)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (I5P2_HUMAN | P32019)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0052659    inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate.
    GO:0052658    inositol-1,4,5-trisphosphate 5-phosphatase activity    Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + H2O = 1D-myo-inositol 1,4-bisphosphate + phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004439    phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030317    flagellated sperm motility    Any process involved in the controlled movement of a flagellated sperm cell.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0070613    regulation of protein processing    Any process that modulates the frequency, rate or extent of protein processing, any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        I5P2_HUMAN | P320193n9v 4cml 5a7i 5a7j

(-) Related Entries Specified in the PDB File

3n9v 3nr8